ROOT
by Vacant Muse
Summary: Naruko Uzumaki is entrusted to Danzo Shimura by the council on the day of the Kyuubi's attack, against the Sandaime Hokage's wishes. Will Naruko bend to Danzo's control? Or will she become the hero Konoha so dearly needs. Fem!Naruto, ROOT!Dark!Naruko!
1. Indoctrination

AN: This fic might get a bit dark at times, but I think that's appropriate, given ROOT's nature.

* * *

**ROOT**

Indoctrination

* * *

"_This child should be treated as a hero, as the Yondaime requested!"_

"_A Jinchuuriki is a powerful weapon Hiruzen, we should use it as such."_

"_I will not allow it! She is a child! An innocent child! Not a weapon! She is the only surviving heir of the Namikaze and Uzumaki clans, she is a hero, we should treat her as such!"_

"_If we cannot come to an agreement, perhaps we should bring the matter before the council. They will make the right choice, and I will abide by it, regardless of the outcome."_

"_This is foolish Danzo!"_

"_Let the council decide that, hm?"_

"_...Very well. The council will see reason."_

"_I agree."_

* * *

The girl awoke with a start, sitting upright, her breathing short and rapid. Her body was drenched in sweat.

"More dreams?" She looked at the speaker, an old man, his black hair shaggy and his face bandaged.

"Y-yes, Danzo-sama." The man nodded, and placed a hand on her shoulder. A small smile appeared on his face, and Naruko felt safe.

"We've discussed this, Naruko-chan, your dreams are not dreams, they are memories."

"Y-yes. Sp-sp-spo-" Her body still felt heavy from sleep, and her mouth couldn't keep up with her brain.

"You're looking for sporadic."

"Y-yes! Sporadic...editet...memory." Her face was screwed up in concentration.

"Eidetic. Sporadic eidetic memory. Almost correct Naruko-chan."

The girl pouted, and Danzo laughed. "I almost had it."

"Yes, yes you did. You are barely seven Naruko, it is understandable that you cannot remember everything perfectly. Perhaps, in time, with training, we shall be able to drop the sporadic from your memory, yes?"

She nodded vigorously.

"Now then, would you kindly get yourself ready for training? You will be meeting your partner today." He watched her carefully for a reaction. She did not disappoint.

"P-partner? Like...like niisan?" Naruko wished that her sporadic memory thing hadn't chosen that event as one to record. She sometimes woke up with the feel of blood in her mouth and hands on her throat, then the pressure suddenly lessened, and she woke screaming and sobbing. As always, Danzo was at her bedside, waiting to console her.

Danzo smiled down at her, "No, not like that. Koi-chan is to be your partner, your permanent partner. At least until one of you expires."

Expires. Like milk going bad. So impersonal. Disconnected. The tone gave Naruko a taste in her mouth, not entirely unlike spoiled milk. "Yes."

"Do you have any questions?"

Naruko ceased fumbling with the strap that would hold her tanto to her lower back. "Is she clanless? Like me?"

The old man's unbandaged hand went to his chin, and his eyes closed. "Hmmm." Naruko associated that sound with lies. They tasted saccharine. Sweet, but overly so. "No, she is from a clan, but her parents both expired in the field."

The spoiled milk taste overpowered the cloying taste of lies. "What clan?"

"Nara. She was renamed accordingly."

"Mmm. Koi. Written as with dark?"

"Correct." Praise. Cinnamon. Naruko beamed. She knew when Danzo was lying to her, when he was keeping secrets, but he had always been there for her, consoling her, teaching her, making her strong. She owed him her life, and he asked only that she use it in service to Konohagakure.

Because of what she owed Danzo, she would gladly do so.

The walk to where her new partner waited was short, and Naruko heard the sound of muffled sobbing as they approached the room. It tasted like...plums? Her own crying never evoked a reaction, so it was a new sensation to her. The door opened, and Naruko was allowed to enter.

The girl was tiny, her face gaunt and her stomach sunken. A brief jolt of disgust shot through her. ROOT had been starving her, to make her react more favorably to the first person to bring her food. The thought was confirmed as Danzo placed a fruit in her hand. A plum, by the feel of it. Without hesitating, she offered it to the terrified girl.

"You're hungry? Right? Take it. It's good." She took a bite out of the plum. "See?" The girl snatched it from her hands, and in seconds, had reduced it to a bare pit, and was occupied with licking the juice off her fingers. Smiling, Naruko turned to Danzo, "Do we have more Danzo-sama?"

The old man nodded, and a ROOT member seemingly materialized with a basket of food, which Naruko gladly took.

"Does she...know her name?" She kicked herself mentally. Danzo would note her hesitation, and she would pay for it later. She would probably be subjected to one of Fū's...sessions. A shudder went through her body, which Danzo no doubt noticed. Which meant a double session.

"No, she does not. I will leave it to you to remedy that. Bond with her. She _is_ to be your partner after all."

"Yes Danzo-sama." Naruko began to turn towards the starving girl before Danzo spoke.

"And Naruko?" There was a chill to his voice. It tasted bitter.

"Yes?"

"Report to Fū before you prepare for sleep. He will be informed that you are coming."

"Yes, Danzo-sama."

The door closed with a sort of finality.

"Of course...Danzo-sama." Naruko moved towards the girl, pulled her into her arms, and held her close while she ate. "Welcome to ROOT, Koi-chan."

"No." The girl muttered her refusal between mouthfuls. "Hanaka."

"I'm sorry...they usually bring recruits in when they're younger...your name is Koi now."

The girl struggled against Naruko's embrace, but was too weak to break it.

"I'm sorry. I'm so sorry."

"HANAKA!"

"Shh, shh... I'm so sorry. Please...you need to answer to Koi."

"That's not my name!"

"I know! Just...please...they'll make you forget. They'll make you forget your name...if you refuse to answer to Koi." Naruko released the girl, her arms falling to her side. "They...tried to make me forget. Naruko. That's my name. Naruko. They tried to name me Kin."

"Your hair?"

"I guess...Danzo's idea of a joke I guess." She kept her long blonde hair pulled back into a ponytail. "I can't forget...certain things. We aren't sure why. Something about...brain...chemology? I don't know the word. But they can make you forget. So...let's make a deal...I'll call you Hanaka...in private, and you can call me Naruko...and we both start answering to our ROOT names...Koi and Kin."

"O-ok..." The smaller girl smiled weakly.

"Good! Now eat up! They're gonna put us to work tomorrow. Training and stuff. I'll uh...ask them to move you into my room. I'll...be there later." Naruko rose up and made her way to the door.

"You have to go?" Despair. It tasted like ash.

Naruko grimaced, "Yes. I need to go see the man that makes us forget."

"Why?" Terror. Tastes like bile.

She sighed, and smiled sadly at Hanaka. "So he can destroy a little bit more of who I am."

* * *

"_Hello Kin."_

"_Naruko. My name. It's Naruko."_

"_Of course. Please, have a seat Kin, and we will begin."_

"_Why do you keep doing this?"_

"_Because Danzo-sama commands it. We live to serve Danzo-sama, and to protect Konohagakure."_

"_We can protect it without giving up our names. You had a name."_

"_Danzo-sama gave us new names. Your partner has accepted this. Why do you resist?"_

"_My parents gave me my name."_

"_Your parents are dead."_

"_I've given everything else for Danzo-sama."_

"_Then what is one more thing?"_

"_It's all I have."_

"_You have ROOT."_

"_ROOT has me."_

"_Then give it everything."_

"_Fuck you."_

"_Wrong."_

_Darkness. White. The taste of flowers._

"_What is your name?"_

"_Naruko!"_

"_You answer to your name, when anyone but Danzo-sama or myself calls you by it. Why is that?"_

"_Danzo-sama calls me by my name when none can hear it. You? I just do it to piss you off."_

"_You are strong. I'll give you that. Perhaps it's because of the Kyuubi?"_

"_Never did anything for me."_

"_He-"_

"_Do not speak of him!"_

"_Oh? Perhaps you feel like his apprentice did."_

"_He's a traitor to Konoha, to Danzo-sama, and to ROOT."_

"_Correct."_

_Darkness. White. The taste of flowers._

"_What is your name?"_

"_Naruko!"_

"_I wonder if it _is_ the Kyuubi. I've heard tell of Jinchuuriki resisting genjutsu, and my clan's techniques, because of their Bijuu. It is understandable. No matter. Only Morino-dono is more skilled as an interrogator than myself. If he was a member of ROOT, you would be in his tender care."_

"_I feel so much better now."_

"_You should. His methods are far more invasive than my own."_

"_How is crawling around inside my brain not invasive?"_

"_Hm. Perhaps...my methods...in addition to his? Yes. I think this will work well."_

"_I-I don't think Danzo-sama authorized tha-" Darkness. White. The taste of flowers. The scent of burning flesh. The taste of ashes._

* * *

"I know we're short this year, but team seven should do just fine with two members. After all, Sakura-chan and Sasuke-kun are the top students of the ye-" Iruka stopped mid word, blinking slowly.

As if the entire class had blinked simultaneously, a trio of masked ANBU had appeared, one significantly taller than the others. All three wore black pants and a short, black, half-length jacket, with red bands on the shoulders. The shortest of the trio wore a long-sleeved black under-shirt and had spiky waist length black hair, pulled back into a ponytail, the ANBU's gender was indeterminate, but the ANBU wore a horned mask vaguely reminiscent of a deer. The second ANBU wore a black and gold fox mask, and an orange sleeveless shirt, her waist length blonde hair pulled back into a tight braid. The tallest was swathed in a white cloak, and wore a cat mask. It was the tallest that spoke. "By order of the Hokage, the ANBU trainee named Kin is to become a member of team seven under Kakashi Hatake. Effective immediately."

As if the room had blinked once more, the deer masked ANBU and the cat masked ANBU vanished, leaving only the ANBU named Kin standing before the class. She offered a short bow, and removed her mask, which she clipped onto her belt.

Iruka finally collected himself enough to speak, "Uh. Um. Please, uh, introduce yourself?"

"Yes, Umino-sensei." The girl's face was devoid of emotion, three deep scars carved into each cheek, giving her the appearance of whiskers. Despite the blankness of her face, her bright blue eyes burned with a ferocity seen in far too few. "I am called Kin...and that's what I've been told to tell you. My name is Naruko Uzumaki, and I'd much prefer you call me that."

* * *

AN: Maou here, so, first collaborative story that I've ever written, hope you enjoy it. Please, comment, let us know what worked, what didn't, what pairings you'd like to see, ect.

AN2: Hello! Imber here! I hope you all like my concept, I have to say, I'm much more satisfied with what Maou came up with in his writing, as opposed to whatever I would have. Please, review and all that whatnot!


	2. All That Glitters

AN: Thanks to isee4, ddcj1990, Exleader75, and Ceralyn for their reviews, and thanks especially to Exleader for your comments and advice. Thanks also to all the faves and alerts, your attention keeps us alive.

For all the readers that might be curious, Naruko has Sporadic Eidetic Memory, and a form of Synethesia called Lexical-Gustatory Synesthesia. The former means that she has perfect and total memory of certain, random events and things. Unlike someone with Eidetic Memory, she cannot remember _everything_ with perfect accuracy. Lexical-Gustatory Synesthesia means that, as I'm sure you've gathered, Naruko can _taste_ sounds. Both of these are real things, Google them if you don't believe us.

* * *

**ROOT**

All That Glitters

* * *

"So..."

Naruko looked up from her seat to find Sakura Haruno standing over her. The class had emptied, the jonin sensei of the other teams had long come and gone.

"You're ANBU?"

Naruko blinked languidly. Curiosity. The taste of miso soup. Fascinating. "Yes. Though I am only a trainee, I've never left the village."

The Uchiha broke his silence, his voice was laden with barely concealed fury and despair. Blood and ashes. "You must be skilled. You're already in the ANBU at this age." There was jealousy in his voice. A sour taste.

"You must have graduated early...right?"

Naruko shook her head, enjoying the sensation of Sakura's curiosity before she spoke, "I was never in the Academy. I was raised by my sensei. I'm an orphan you see. I never knew my parents."

"Can you teach me?" Sasuke's blood and ashes voice cut through the air like a blade. Naruko cringed.

"Maybe. We'll have to ask Hatake-sensei. Even then, I'd only be able to show you basic things without consulting with my superiors in ANBU. I have the feeling they wouldn't mind. After all, you're the reason I'm here."

Sasuke frowned, and his voice was flavored with confusion, a faintly bitter taste. "What does that mean?"

Naruko shrugged, "You're the last Uchiha in Konoha. You possess a powerful and valuable kekkei genkai. I'm supposed to do my utmost to ensure that you gain mastery of said bloodline, and keep you from falling into enemy hands."

The door slid open, and a man with messy silver hair, a mask covering the bottom half of his face, and his headband pulled down over one eye walked into the room. In his hand was a bright orange book. His single eye peeked over the book and took stock of the room's occupants. His brow furrowed as he recognized the uniform of Danzo's ROOT ANBU on the blonde.

"My first impression is-"

"I love that book!" The blonde practically shouted, and clapped her hand over her mouth. Clearly, Danzo's conditioning wasn't effective on this one.

"-I hate you all. Except for you Blondie. You have good taste in literature. Be on the roof in five minutes." With that, Kakashi vanished in a swirl of leaves, reappearing on the roof.

With the blonde standing right next to him.

"Slow Kakashi-sensei. I expected more of the infamous Copy-nin." She smirked, and Kakashi glimpsed the tip of a canine tooth. "You must have a small-"

Kakashi cut her off, all to aware of the bizarre things younger members of ROOT often said. "So, why did Danzo send you?" Mentally, he kicked himself. He saw the glimpse of black on her tongue when she spoke, meaning that Danzo's seal was present. Not only would she be unable to talk about her master, or his orders, she would be paralyzed from the attempt."

"Danzo-sama has ordered me to ensure the activation of Sasuke Uchiha's Sharingan, and keep him from falling into enemy hands."

Kakashi blinked. Perhaps he was mistaken, and the girl didn't have Danzo's seal on her tongue.

"You have no ill intentions towards my team?"

The girl smiled, "None at all Kakashi-san. I live to serve Konohagakure. On that note, Sasuke-kun has requested that I teach him what I can from my training. An understandable request, seeing as despite my official ranking, or lack thereof, I am roughly on par with a upperclass Chunin. I told him that I needed to obtain your permission. After all, you are the Jonin sensei of this team, and, despite not being an active ANBU, your ranking was higher than mine, and I will therefore defer to your judgment, lacking orders from Danzo-sama."

Kakashi blinked once more. He wanted to say she sounded like a machine, like that speech was programed into her. It probably was. That didn't change the fact that it sounded genuine, almost earnest. Perhaps that was Danzo's doing, or perhaps she really was genuine. She certainly had more of a personality than Danzo's typical lackeys. He couldn't help but wonder just what skills she did have.

"You have my permission, on the condition that you clear everything with me before showing him."

The girl shrugged, "Understandable. Um..." She was fidgeting. It was somewhat adorable.

"Yes?"

"I have a personal request...well...two."

"They are?"

"I understand that I have a skill level greater than the average genin, but my skills are still...unrefined. I would request that you teach me as you would any other student. Also...do you have volume two of Icha Icha?"

Kakashi smiled beneath his mask. "Of course I do."

* * *

Kakashi was, again, hours late, so Naruko sat silently atop a training post at the designated meeting place. Sasuke sat languidly beneath a tree, and Sakura fawned over him like the overbearing fangirl that she was.

Despite his shortcomings, Naruko had no doubt that Kakashi would prove to be a skilled teacher, and would likely round out her skill set. Danzo had focused largely on assassination techniques and infiltration. She could move unseen and kill a room full of people without any of them noticing, but she didn't have a prayer in an open combat situation. Realistically, she knew that many of the techniques she had learned were perfectly applicable to open combat situations, but ROOT didn't encourage creativity. Linear thought doesn't allow for much room for improvisation. She simply didn't know _how_ to use her techniques in a direct offense. Kakashi was known for his ability to improvise and adapt. Naruko wished, above all else, to add that to her skill set.

Sakura Haruno was all brains and no brawn. Truthfully, Sakura remined Naruko of Hanaka. Without the redeeming features of being useful and adorable. Hanaka could have thought circles around Naruko, having somehow been too intelligent for ROOT's trend of linear thinking to trap her. Combining that with her impressive skills with her shadow techniques, Hanaka and Naruko were, in her opinion, the perfect team. But Sakura had no impressive shadow techniques. She had no redeeming features aside from an impressive memory and above average chakra control, and that control was a result of a below average chakra pool. Perhaps Danzo would allow Hanaka to teach Sakura how to be a proper kunoichi, if Naruko recommended it...but no. Hanaka was in no position to teach anyone.

Sasuke Uchiha. The boy was melancholic, to say the least. She sympathized with him though, he had his family ripped away from him, nobody should have to go through that pain. That aside, his personal issues needed to take second saddle to team efficiency. They needed to mesh together well in order to complete their future missions in an effective and timely fashion.

"So, did you finish volume two?" Despite the suddenness of the voice, it lacked the presence needed to startle the blonde shinobi.

"Not yet. I'm barely on chapter two, after all, Danzo-sama doesn't really approve of my reading such th-" Naruko paused, and sighed. "How did you do that?"

"I'll never tell." Kakashi sounded smug. Coming from him, the taste wasn't unpleasant, not like when Fu was smug. "Time for the test to see if this team will even stay together. Although, I'm sure you have orders to make sure that it does?"

"Danzo-sama never mentioned anything of the sort. However, if this team doesn't pass, undoubtedly I'll be punished. It's in my best interest to prevent that." Kakashi noted that the blonde's fists clenched. He couldn't see her hands beneath her black gloves, but undoubtedly they were scarred, if the marks on her arms were anything to go by. Odd, Danzo wasn't much for invasive indoctrination. Scars could hinder mobility. She stood smoothly and looked towards her inattentive team. "Sensei is here! Form up!"

Kakashi imagined Naruko's idea of forming up is an orderly formation, executed swiftly and silently. What she got was Sasuke's indifferent amble towards the training posts, accompanied by Sakura's incessant chatter. Still, the blonde took charge and explained that they would be participating in a sort of survival test, the result of which would decide whether or not the team would be allowed to remain together, or if they would be sent back to the academy. She then dropped down from her perch and stepped into line with Sasuke and Sakura.

Kakashi nodded sagely, his face still hidden behind his book and mask. "You task, is to get these bells from me." He held up two dented bells, and tied them to his belt. "There are only two bells, so that means that only two of you can pass." Naruko cursed under her breath, and Kakashi couldn't keep himself from grinning. "Of course, to get them from me, you should come at me with the intent to kill. You have until lunchtime. Good luck!" With that, the cyclopian shinobi vanished in a swirl of leaves.

Sasuke and Sakura moved to dash off, only for Naruko's hands to latch firmly onto their shoulders. "The point of the mission is teamwork. We have to work together. I'm more skilled than the both of you, and I've got no hope against someone like him on my own. There are two bells. One for each of you. Regardless of anything else, you two need to pass. After all, you're Team Seven. I'm just your quirky hanger-on, right?" The pair looked at her like she was crazy. "Will you work with me?"

Sakura looked to Sasuke for guidance, and the Uchiha nodded.

From the looks on their faces, Naruko gathered that the smile on hers was quite fierce.

* * *

"_Sit."_

"_Danzo-sama?"_

"_Please, would you kindly be seated, Naruko-chan."_

"_Yes Danzo-sama."_

"_Good."_

"_How have your sessions been?"_

"_They hurt."_

"_The seal?"_

"_Everything. The fox rebels against it. It doesn't want to allow these things."_

"_You are the master. Not the Kyuubi."_

"_And you are my master."_

_Saccharine sweetness._

"_Danzo-sama. Why do you allow that man so much independence?"_

"_He is useful."_

"_What about Kabuto-san? Do you intend to go through with it?"_

"_Do you have an opinion on the situation?"_

"_You say he's gotten too effective. Does that diminish his loyalty?"_

"_What are you-"_

"_If Koi gets too effective, will you have her eliminated? What about me? Fu? All of us? We serve you, we serve Konoha, but we are alive. We are loyal to our last breath. What gives you the right to decide when we're no longer of use? When we're _too effective_ to be controlled?"_

"_Be silent."_

"_I will not!"_

"_Would you kindly take your seat and be silent."_

_The taste of flowers, a cottony feeling inside._

"_Good. You're expected to report for another session. I understand he's made progress in enhancement seals. Your resilience to the...negative effects make you the perfect subject for initial trials."_

_A cottony feeling inside._

"_I see you don't object. I apologize for any pain the application process might cause you, but it is a necessary evil. You are dismissed, would you kindly report to his labs?"_

_The taste of flowers, a cottony feeling inside. "Yes Danzo-sama."_

* * *

"They're chasing Tora, Hokage-sama."

The Hokage sighed, that cat was the most hated thing in the village, bar none. There were, however, more pressing matters that needed his attention. Namely, the sudden reappearance of Naruko Uzumaki, clearly a member of Danzo's supposedly disbanded ROOT organization.

"What do you think Kakashi-kun?"

The jonin rubbed his chin, "Unlike everything we've seen of Danzo's pet weapons, she seems very much like her parents. More subdued than either of them, but similar. She very clearly said that her codename at ROOT is Kin, but that her _name_ is Naruko. She knows who she is. She's very clear that unless Danzo gives specific orders on an issue, she'll defer to my judgment, or lacking that, will follow what she feels to be the best course of action."

The Hokage nodded thoughtfully, lighting his pipe as he did. "Do you think it is intentional on Danzo's part? Or is she simply that strong?"

"I'm inclined to believe the latter. Any child of theirs would definitely be stubborn as a rock."

The Hokage cleared his throat, in an attempt to cover his laughter, then scowled. "The council moves behind my back yet again Kakashi." The old man sighed. "I'm far too old for this Kakashi-kun. What am I to do?"

"Show that you are not an old man to be bullied by bureaucrats and merchants. You are the Professor. The Sandaime Hokage. And you are the very best of us." Kakashi's voice was even, icy.

"If I am the best of us... then what is Danzo?"

"The very worst." The reply came quickly, without hesitation.

"I disagree...I have never approved of his methods, but he has, and ever will be, Konoha's loyal servant."

"Only if he gets to decide how he should best serve Hokage-sama."

"All too true."

Kakashi stood silent as the Hokage puffed on his pipe.

"Tell me, Kakashi-kun. How does one stop a dog from tugging overmuch on the leash?"

"I've never been one for leashes, to be honest."

"I have noticed that."

Kakashi sighed. "I think, Hokage-sama, that the answer is to give the dog a longer leash."

"But with a longer leash, the dog can turn and bite his master."

"Then a longer leash, and a muzzle."

"How would I lengthen his leash Kakashi-kun, when he has slipped it entirely."

"Order the formal reestablishment of ROOT, and make it answer only to you."

The Hokage nodded slowly, a small smile creeping across his lips. "That is the leash. What of the muzzle?"

Kakashi shook his head. "I don't know Hokage-sama."

"You will take position alongside Shikaku Nara as one of Konoha's Jonin Commanders, and will take position as the head of the ANBU. You are the muzzle Kakashi-kun. We will give him a longer leash. We just need to keep him from biting."

* * *

AN: So, I kinda wrote the last bit of the chapter while I was watching Game of Thrones, don't know if that sort of bled into my narrative. In any case, review and comment please.


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